2011-08-25 23:07:08 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>fix restrain command
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</H3>
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<P><B>Syntax:</B>
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</P>
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2012-05-22 21:56:16 +08:00
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<PRE>fix ID group-ID restrain keyword args ...
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2011-08-25 23:07:08 +08:00
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>restrain = style name of this fix command
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2012-05-22 21:56:16 +08:00
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<LI>one or more keyword/arg pairs may be appended
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2011-08-25 23:07:08 +08:00
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2012-05-22 21:56:16 +08:00
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<LI>keyword = <I>bond</I> or <I>angle</I> or <I>dihedral</I>
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2011-08-25 23:07:08 +08:00
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2012-05-22 21:56:16 +08:00
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<PRE> <I>bond</I> args = atom1 atom2 Kstart Kstop r0
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atom1,atom2 = IDs of 2 atoms in bond
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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2012-05-22 22:16:17 +08:00
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r0 = equilibrium bond distance (distance units)
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<I>angle</I> args = atom1 atom2 atom3 Kstart Kstop theta0
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2012-05-22 21:56:16 +08:00
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atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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2012-05-22 22:16:17 +08:00
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theta0 = equilibrium angle theta (degrees)
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2014-05-03 05:47:08 +08:00
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<I>dihedral</I> args = atom1 atom2 atom3 atom4 Kstart Kstop phi0
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2012-05-22 21:56:16 +08:00
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atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
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Kstart,Kstop = restraint coefficients at start/end of run (energy units)
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2012-05-22 22:16:17 +08:00
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phi0 = equilibrium dihedral angle phi (degrees)
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2011-08-25 23:07:08 +08:00
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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2012-05-22 21:56:16 +08:00
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<PRE>fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
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fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
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fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
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fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0
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2011-08-25 23:07:08 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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2012-05-22 21:56:16 +08:00
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<P>Restrain the motion of the specified sets of atoms by making them part
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2012-05-22 22:16:17 +08:00
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of a bond or angle or dihedral interaction whose strength can vary
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over time during a simulation. This is functionally equivalent to
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creating a bond or angle or dihedral for the same atoms in a data
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file, as specified by the <A HREF = "read_data.html">read_data</A> command, albeit
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with a time-varying pre-factor coefficient. For the purpose of
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forcefield parameter-fitting or mapping a molecular potential energy
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surface, this fix reduces the hassle and risk associated with
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modifying data files. In other words, use this fix to temporarily
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force a molecule to adopt a particular conformation. To create a
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permanent bond or angle or dihedral, you should modify the data file.
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</P>
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<P>The group-ID specified by this fix is ignored.
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</P>
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<P>The second example above applies a restraint to hold the dihedral
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angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant
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restraint coefficient. The fourth example applies similar restraints
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2011-08-25 23:07:08 +08:00
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to multiple dihedral angles using a restraint coefficient that
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increases from 0.0 to 2000.0 over the course of the run.
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</P>
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<P>IMPORTANT NOTE: Adding a force to atoms implies a change in their
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potential energy as they move due to the applied force field. For
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dynamics via the <A HREF = "run.html">run</A> command, this energy can be added to
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the system's potential energy for thermodynamic output (see below).
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For energy minimization via the <A HREF = "minimize.html">minimize</A> command, this
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energy must be added to the system's potential energy to formulate a
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self-consistent minimization problem (see below).
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</P>
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<P>In order for a restraint to be effective, the restraint force must
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typically be significantly larger than the forces associated with
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2012-05-22 22:16:17 +08:00
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conventional forcefield terms. If the restraint is applied during a
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2011-08-25 23:07:08 +08:00
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dynamics run (as opposed to during an energy minimization), a large
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restraint coefficient can significantly reduce the stable timestep
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size, especially if the atoms are initially far from the preferred
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conformation. You may need to experiment to determine what value of K
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works best for a given application.
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</P>
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<P>For the case of finding a minimum energy structure for a single
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molecule with particular restratins (e.g. for fitting forcefield
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parameters or constructing a potential energy surface), commands such
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2012-05-22 22:16:17 +08:00
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as the following may be useful:
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2011-08-25 23:07:08 +08:00
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</P>
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<PRE># minimize molecule energy with restraints
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velocity all create 600.0 8675309 mom yes rot yes dist gaussian
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fix NVE all nve
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fix TFIX all langevin 600.0 0.0 100 24601
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2012-05-22 22:16:17 +08:00
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fix REST all restrain dihedral 2 1 3 8 0.0 5000.0 $<I>angle1</I> dihedral 3 1 2 9 0.0 5000.0 $<I>angle2</I>
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2011-08-25 23:07:08 +08:00
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fix_modify REST energy yes
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run 10000
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fix TFIX all langevin 0.0 0.0 100 24601
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2012-05-22 22:16:17 +08:00
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fix REST all restrain dihedral 2 1 3 8 5000.0 5000.0 $<I>angle1</I> dihedral 3 1 2 9 5000.0 5000.0 $<I>angle2</I>
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2011-08-25 23:07:08 +08:00
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fix_modify REST energy yes
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run 10000
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# sanity check for convergence
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minimize 1e-6 1e-9 1000 100000
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# report unrestrained energies
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unfix REST
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run 0
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</PRE>
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<HR>
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2012-05-22 22:16:17 +08:00
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<P>The <I>bond</I> keyword applies a bond restraint to the specified atoms
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using the same functional form used by the <A HREF = "bond_harmonic.html">bond_style
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harmonic</A> command. The potential associated with
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the restraint is
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</P>
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<CENTER><IMG SRC = "Eqs/bond_harmonic.jpg">
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</CENTER>
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<P>with the following coefficients:
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</P>
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<UL><LI>K (energy/distance^2)
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<LI>r0 (distance)
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</UL>
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<P>K and r0 are specified with the fix. Note that the usual 1/2 factor
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is included in K.
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</P>
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<HR>
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<P>The <I>angle</I> keyword applies an angle restraint to the specified atoms
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using the same functional form used by the <A HREF = "angle_harmonic.html">angle_style
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harmonic</A> command. The potential associated with
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the restraint is
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</P>
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<CENTER><IMG SRC = "Eqs/angle_harmonic.jpg">
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</CENTER>
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<P>with the following coefficients:
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</P>
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<UL><LI>K (energy/radian^2)
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<LI>theta0 (degrees)
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</UL>
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<P>K and theta0 are specified with the fix. Note that the usual 1/2
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factor is included in K.
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</P>
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<HR>
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2011-08-25 23:07:08 +08:00
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<P>The <I>dihedral</I> keyword applies a dihedral restraint to the specified
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2012-05-22 22:16:17 +08:00
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atoms using a simplified form of the function used by the
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<A HREF = "dihedral_charmm.html">dihedral_style charmm</A> command. The potential
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associated with the restraint is
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2011-08-25 23:07:08 +08:00
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</P>
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<CENTER><IMG SRC = "Eqs/dihedral_charmm.jpg">
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</CENTER>
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<P>with the following coefficients:
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</P>
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2012-05-22 22:16:17 +08:00
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<UL><LI>K (energy)
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2011-08-25 23:07:08 +08:00
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<LI>n = 1
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2012-05-22 22:16:17 +08:00
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<LI>d (degrees) = phi0 + 180
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2011-08-25 23:07:08 +08:00
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</UL>
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2012-05-22 22:16:17 +08:00
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<P>K and phi0 are specified with the fix. Note that the value of n is
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hard-wired to 1. Also note that the energy will be a minimum when the
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current dihedral angle phi is equal to phi0.
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</P>
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2011-08-25 23:07:08 +08:00
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<HR>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>.
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</P>
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<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
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fix to add the potential energy associated with this fix to the
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system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
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output</A>.
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</P>
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<P>IMPORTANT NOTE: If you want the fictitious potential energy associated
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with the added forces to be included in the total potential energy of
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the system (the quantity being minimized), you MUST enable the
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<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
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</P>
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<P>This fix computes a global scalar, which can be accessed by various
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2011-08-26 01:01:01 +08:00
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<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
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2012-05-22 22:16:17 +08:00
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potential energy for all the restraints as discussed above. The scalar
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value calculated by this fix is "extensive".
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2011-08-25 23:07:08 +08:00
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command.
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</P>
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2012-05-22 22:16:17 +08:00
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<P><B>Restrictions:</B> none
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2011-08-25 23:07:08 +08:00
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</P>
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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